You don't have to repack the upstream tarball to strip the debian directory. (The debian directory is automatically replaced by the content of the .debian.tar.{gz,bz2,lzma,xz} file at unpack time)

Debian-specific changes are no longer stored in a single .diff.gz but in multiple patches in debian/patches/. It is compatible with quilt (hence its name) but does not require its usage as dpkg-source is able to do everything needed by itself. It applies patches at extraction time and update the patch series at build time.

When you switch to "3.0 (quilt)", there are other changes that you might want to do:

If your .diff.gz modifies upstream files, you should really put those changes in separate quilt patches first, otherwise all those changes will be merged in a single quilt patch named debian/patches/debian-changes-<version>. Consider documenting those patches by following DEP-3.

If you use another patch system (dpatch, dbs, cdbs, etc.; with -p0, -p1, or p2), consider switching to the "3.0 (quilt)" format (see 581186 for a conversion helper script). (You can then simplify your debian/rules with "dh $@", see next point).

You should remove everything related to quilt in debian/rules (patch/unpatch logic, cleanup of quilt stamp file and its .pc directory).

Does a 3.0 (quilt) source package need to build-depend on quilt?

No because you're supposed to remove the quilt usage in debian/rules (patch/unpatch logic).

Is the README.source file needed with 3.0 (quilt) source packages?

No. Since dpkg-source -x applies the patch, you don't have to explain how the patch system works. If lintian gives you the patch-system-but-no-source-readme warning, upgrade to the latest version in sid.

How to use multiple upstream tarball in 3.0 (quilt) format?

Simply put a file <source>_<version>.orig-<component>.tar.{gz,bz2,lzma,xz} near the traditional .orig tarball. The content of that tarball should also be already unpacked in the component subdir of the unpacked source package. The next dpkg-source -b will pick it up automatically.

any upstream contributor is more likely to find and merge the patches (if you haven't forwarded it properly)

other distributions can reuse our patches

even if you don't have any upstream patch right now, next time that someone must NMU your package, they can cleanly add a patch (with a proper DEP-3 header) without having to modify the build system

same applies for derivative distributions that have to modify your packages... you're more likely to be able to find something valuable to merge if their changes are kept as separate patches instead of merged within the .diff.gz

debian/rules can be simplified by getting rid of the patching/unpatching code (or the uuencoding/uudecoding code if you ship a supplementary binary file like an icon)

the upstream tarball is bzip2-compressed and you don't want to have to convert it

the upstream tarball contains a debian directory and you don't want to repackage it just to remove that directory

the upstream author releases the software in multiple tarballs

you don't have to add -i -I every time that you manually build the package from the VCS repository (the VCS-specific files are ignored by default)

in the long run it's best to standardize on a single patch system (new contributors need to learn a single system, more people can help you, etc.) and quilt appears to be that patch system.

I get lintian errors and warnings with new source formats

The following warnings are incorrect for the new Debian source formats, and are fixed in the latest Lintian:

I converted my package but it fails to build or fails to unpack on all buildds

You probably have quilt patches that only applies with fuzz (i.e. they only apply if patch ignores context lines). quilt applies those without failing but dpkg-source doesn't. The solution is to refresh the patches, for example with those commands :

quilt pop -a
while quilt push; do quilt refresh -p ab; done

dpkg-dev 1.15.5.3 and later prevent you from building source packages with such patches.

Please try using new source packages with all your usual tools (in particular if you maintain them) and file bugs if you encounter problems and usertag them appropriately (user hertzog@debian.org / tag 3.0-quilt-by-default). Also update the list above with any relevant information (including pointers to bugs).